Ever since I started using computers, I've been baffled by the relative clumsiness of installing applications. Whether we are talking the really old days (launching the Rambo game off a tape), the '90s (running Keen or using installers in Windows 95), or the modern days (still those installers, but now also package management and self-contained applications); it's all relatively cumbersome, and they all have their downsides. I decided to put my money where my mouth is, and come up with my idealistic, utopian method of installing, running, updating, and uninstalling applications.

Nice try, Thom - if you're just reading it casually you almost miss the hand-waving about binaries that don't belong in any particular 'program bundle',

Miss? It's right there in the article:

"I also took a cue from Mac OS X by creating the specific /System/Utilities directory, where the operating system can store utilities such as the Activity Monitor, graphical Bluetooth tools, Network Utilty (graphical ping, whois, etc.), those sorts of things. What does and doesn't go into that directory is fairly arbitrary, and is open for debate. Other binaries that usually reside in /bin on UNIX systems can also go into /System (say, something like /System/Binaries, since this is the 21st century - why use unclear acronyms)."